Saliva is an important determinant of oral health and contains a large number of proteins and peptides that keep oral cavity in good working order. One remarkable feature of saliva is its potent antimicrobial activity against a wide array of invading pathogens such as human immunodeficiency virus type I (HIV-1), the fungus Candida albicans, and a large number of bacteria associated with oral and systemic diseases. However, little is known regarding the overall protein species present in saliva and its changing pattern over the course of HIV-1 infection, largely due to the insensitivity and limited reproducibility of traditional techniques. It is the goal of this application to adapt the state-of-the-art proteomic-based technique, ProteinChip and multidimensional protein identification chromatography (MudPIT) technologies, to determine differences in salivary protein profiles in HIV-negative and HIV-positive individuals before and after high actively antiretroviral therapy (HAART). We also propose to characterize salivary protein isoforms, structural modifications, and concentrations of selected biomarkers altered in HIV-1 infection and to establish a relational database for storage and statistical analysis of these data. The central hypothesis of this project is that the profile of salivary proteins will be altered in HIV infection and will restore toward normal levels after HAART. The uniqueness of our current proteomic approach is the integration of a surface-enhanced laser desorption/ionization (SELDI) technology and MudPIT. It can simultaneously compare protein expression profiles from multiple samples within days at the sensitivity of femtogram level, thereby offering the most comprehensive overview with the greatest sensitivity ever achieved as to the changes in identity and quantity of proteins in saliva samples in normal and disease settings. We strongly believe that results from this project will contribute significantly towards our understanding of the salivary response to HIV-1 infection and facilitate identification of novel antiretroviral factors for use as novel diagnostic, oral microbicides or therapeutics against HIV-1 infection.